Install Python 3 Distributions on a Linux Server

As a data scientist, I often need to run Python scripts on Linux servers. The vast majority of CentOS/RHEL-based Linux servers use Python 2.6.6, while most of my Python applications are written in Python 3. In additoin, on most of the servers, I don’t have the sudo priviledge, so it needs a little trick to install Python 3 on those servers.

This post is a step-by-step instructions on installing Python 3.6 through both Anaconda and Python Gzipped source tarball file on a CentOS/RHEL-based Linux server.

Anaconda is the most popular Python distribution platform with a collection of more than 1,000 open source packages, which will be included almost any package you are going to need for data sceince and development. The included environment and package management funcitons make the benefits obvious. However, the big volume (ususally more than 4G) of the installation makes it impossible to install on some servers that you are not allowed to save such big volume files. In these cases, you might want to install Python 3 with only limited necessary packages. Then the Python Tarball file approach described below will do the work.

Check Python Version

Chances are Python is already installed on your Linux server, you can use following commands to check which version of Python has been installed:

$ python --version

$ python -V

Most of the cases, Python 2.x is installed. Then you can install Python 3 by taking following steps.

Instal through Anaconda

Download Anaconda

You can download the latest Anaconda installer from Anaconda Download page. At the time of writing, the latest version is 5.0.1 for Python 3.6.

From the folder where you want to save the installer, you can use curl to download the link that you copied from the Anaconda website:

$ curl -O https://repo.continuum.io/archive/Anaconda3-5.0.1-Linux-x86_64.sh

It will take a while to download.

Verify(Optional)

Once the downloading process is done, you can verify the data integrity of the installer with MD5 or SHA-256cryptographic hashes:

$ md5sum Anaconda3-5.0.1-Linux-x86_64.sh

$ sha256sum Anaconda3-5.0.1-Linux-x86_64.sh

You can check the output against the hashes available for your appropriate Anaconda version at the page of Anaconda with Python 3 on 64-bit Linux. If the MD5 or SHA-256 hash that you generate does not match the one there, the file may not have downloaded completely, you might need to download it again and re-check.

Install Anaconda

Now you can run the script to install:

bash Anaconda3-5.0.1-Linux-x86_64.sh

You should see the following output:

Output

Welcome to Anaconda3 5.0.1 (by Continuum Analytics, Inc.)

In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue

Press ENTER to continue and then continue press ENTER to review the license. Once you’re done reading the license, you’ll be prompted to agree to license terms:

Output
Do you approve the license terms? [yes|no] 

After type yes, you’ll be prompted to choose the location of the installation.

Output
Anaconda3 will now be installed into this location:
/home/lf/anaconda3

  - Press ENTER to confirm the location
  - Press CTRL-C to abort the installation
  - Or specify a different location below

You can press ENTER to accept the default location, or specify a different location to modify it.This the tricky part, because you are installing on a server you have to choose a place where you have appropriate permissions and volume capacity. The the installation process will start copying files and installing required modules to your specified location.

Once it’s complete you’ll receive the following output:

Output
...
installation finished.
Do you wish the installer to prepend the Anaconda3 install location
to PATH in your /home/lf/.bashrc ? [yes|no]
[no] >>>

Type yes so that you can use the conda commandline.

Next, run following activate the installation:

source ~/.bashrc

Once you are finished, you can verify the installation by running:

conda --version

You’ll receive the version number of the isntalled conda. Now the Anaconda is installed, you can check my another post(Managing Python Environments and Packages with Anaconda) for setting and mangeing Python environments and packages.

Install through Tarball File

You can install pure Python 3 distribution through following steps.

Download Tarball File to Your Server

Go to the folder where you want to save the file (e.g./home/lf/) and run:

$ wget https://www.python.org/ftp/python/3.6.4/Python-3.6.4.tgz

It will download the tarbile from Python’s download page.

Verfiy (optional)

After download, you can verify the data integrity through running MD5 hash

$ md5sum Python-3.6.4.tgz

You should compare the output to the result on the download page. As long as you get the same result, you are good to move ahead.

Install

Decompress the file with the following command, which will create a directory /home/lf/Python-3.6.4 and automatically copy all files into this directory. After decompression, the Python-3.6.4.tgz file can be deleted.

$ tar xvzf Python-3.6.4.tgz

When the decompression is done, go into the created folder(/home/lf/Python-3.6.4) and install the new version of Python:

$ ./configure --prefix=$HOME/.local

This step sets up your configuration and makes files.

Then run the command:

$ make

and follow that up with:

$ make install

The last command will install two of the most useful Python utilities:

pip: Python’s recommended tool for installing Python packages.
setuptools: Enables you to download, build, install, and uninstall Python packages.

Add Path to Evironment

Go back to your home folder and open the .bashrc file:

$ cd $HOME
$ nano .bashrc

with the editor open, add the following lines, and save the file:

# Python 3.6.4 
export PATH="$HOME/.local/bin:$PATH"

Run the following to get your environment up to date:

$ source ~/.bashrc

Now the Python 3 has been installed. You can verify the installation through running:

$python3 --version

Wait, why use python3 not just python? If you try the command with python the output will be the version number for the default Python on your Linux server, but the newly installed version of Python. Because you now have two versions of Python on your server. The best way to handle this is to use Python’s virtualenv module, Virtualenv, to create a virtual Python environment. Virtualenv is a tool to create isolated Python environments. The secret to virtualenv is tricking your computer into looking for and installing packages in the project directory rather than in the main Python directory, which allows you to keep them completely separate.

Create Virtual Python Environment

For python 3, since virtualenv are bundled with pythons with 3.4 and after. So you can run

python3 -m venv myPy3Env

to create the environment.

Then you can use following commands to activate and deactivate the built virutal environment.

source  env/bin/activate  # to activate environment
deactivate # to deactiate current environment

After activating an evironment, you can use pip to install packages for the activated environment, for example,

pip install --user numpy

For more on the basics of using virtualenv, see the tutorial on Python Virtual Environments.

References

https://www.digitalocean.com/community/tutorials/how-to-install-the-anaconda-python-distribution-on-ubuntu-16-04

https://hostpresto.com/community/tutorials/how-to-install-anaconda-python-on-ubuntu-16-04/

https://www.digitalocean.com/community/tutorial_series/how-to-install-and-set-up-a-local-programming-environment-for-python-3

https://www.godaddy.com/garage/how-to-install-and-configure-python-on-a-hosted-server/